High-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice provides novel insight on the impact of host genetics

Determining the forces that shape diversity in host-associated bacterial communities is critical to understanding the evolution and maintenance of meta- organisms. To gain novel insight on the genetics of gut microbial traits, we employed a powerful approach using inbred lines derived from the hybrid zone of two incipient house mouse species. We identify a high number of mucosa-associated bacterial taxa with significant heritability estimates, particularly for 16S rRNA transcript-based traits. Interestingly, heritability estimates also positively correlate with cospeciation rate estimates. Association mapping identifies 443 loci influencing 123 taxa, whose narrow genomic intervals enable promising individual candidate genes and pathways to be pinpointed. These results indicate a unique genetic architecture for cospeciating taxa, a clear enrichment for several classes of human disease, and identify important functional categories including innate immunity and G-protein-coupled receptors, whose role in host-microbe interactions diverge as new species form.

Genetic Dissection of the RNA Polymerase II Transcription Cycle

How DNA sequence affects the dynamics and position of RNA Polymerase II during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, which was composed of both existing and novel DNA sequence motifs, and allowed us to redefine molecular models of core transcriptional processes. Our results implicate the strength of base pairing between A-T or G-C dinucleotides as key determinants to the position of Pol II initiation and pause. We reveal substantial differences in the position of transcription termination, which frequently do not affect the composition of the mature mRNA. Finally, we identified frequent, organ-specific changes in transcription that affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.

Meiotic epigenetic factor PRDM9 impacts sperm quality of hybrid mice

Reduced fertility of male mouse hybrids relative to their parents, or hybrid sterility, is governed by the hybrid sterility 1 (Hst1) locus. Rescue experiments with transgenes carrying sequences within or near Hst1 manifested that Hst1 contains the gene encoding meiosis-specific histone methyltransferase PRDM9. The Prdm9 gene is responsible for partial meiotic arrest, testicular atrophy, and low sperm count in (C57BL/6J x PWD)F1 mouse hybrids. Here we report that these male hybrids suffer an additional reproductive disadvantage, decreased sperm quality, which is (i) further exacerbated by the introduction of long transgenes carrying sequences from Hst1 with incomplete Prdm9 into their genome and (ii) controlled by the Prdm9 dosage. These transgenic male hybrids displayed the features of severe oligoasthenoteratozoospermia (OAT), a human infertility syndrome characterized by a low number of spermatozoa with poor motility and morphological abnormalities. Analysis of spermiogenesis in these mice revealed acrosome detachment, aberrant elongation and condensation of the nucleus. As a result, the transgenic sperm had acrosome malformations, abnormal chromatin packaging, and fragmented DNA with elevated base oxidation, revealed by using multiple methods. Heterozygosity for one null Prdm9 allele improved meiotic progression and sperm quality of both non- and transgenic hybrids. Our results indicate that genomic analysis of OAT patients should include consideration of allelic variants in PRDM9, and our transgenic models can serve as tools to understand the diverse molecular processes that, when perturbed, can cause this disease.

Assessment of the Knowledge, Perceptions, and Reactions towards the African Apefly (Spalgis lemolea lemolea) in Tanzania

This paper reports on farmers’ knowledge, perceptions, and reactions towards the African apefly (Spalgis lemolea lemolea), which appeared to be associated with some vegetables in some locations in Tanzania. Information was obtained from a sample of 100 key respondents using a semi-structured questionnaire and from focus groups selected from key locations in five districts in the country with histories with the African apefly. Acute and sub-acute toxicity tests of the African apefly were performed on female Swiss hybrid mice (Mus musculus) to assess whether or not the African apefly was toxic to mammals. The mice were exposed to increasing apefly meal concentrations in acute and sub-acute tests, and signs of toxicity were observed for 14 and 28 days, respectively. Blood samples were collected by cardiac puncture for hematological and biochemical analysis. Gross and microscopic examinations of the internal organs were done. The survey results showed that 92.1% of the respondents perceived the African apefly as poisonous and had stopped consuming the vegetables associated with it. In the toxicity tests, however, no death or toxic signs were displayed, and there was no significant difference between the control and treated mice in weight, hematological parameters, and histo-pathological examination results. These findings strongly indicate that, despite the negative perception by farmers regarding the African apefly, it is not poisonous. However, further studies on how farmers can be trained to have a positive perception of the African apefly and how the insect can be conserved for further research regarding its role in Tanzania are recommended.

Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse

Most mammalian genomes are diploid and previous studies have extensively investigated the average epigenetic profiles of homologous chromosomes. Here we use hybrid mice to distinguish the epigenetic status and three-dimensional organization of homologous chromosomes. We generated Hi-C, ChIP-seq and RNA-seq datasets from CD4 T cells of B6, Cast and hybrid mice, respectively, and systematically analyzed the 3D nucleus organization and epigenetic regulation. Our data indicate that the inter-chromosomal interaction patterns between homologous chromosomes are similar and the similarity is highly correlated with their allelic co-expression levels. Construction of 3D nucleus based on allele-specific interaction frequency revealed symmetric positioning of homologous chromosomes in the 3D nuclear space. The inter-chromosomal interactions at centromeres are significantly weaker than those at telomeres, indicating positioning of centromeres toward the inside of chromosome territories and telomeres toward the surface of chromosome territories. The majority A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments due to cis-effect. About 95% of the trans-effected B6/Cast divergent compartments converge to same compartment status potentially due to a shared cellular environment. We found the differentially expressed genes between the two haploids in hybrid were associated with either genetic associated cis-effects or epigenetic associated trans-effects. The widespread epigenetic differences between B6 and Cast suggest that epigenetic changes may be major contributors to differences between B6 and Cast. Our data revealed symmetrical positioning of homologous chromosomes in 3D nucleus and enhanced our understanding of allele-specific epigenetic regulation.